FMO DATABASE

FMODB ID: 6NL8Z

Calculation Name: 4DZO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DZO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y6D9

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-873794.392778
FMO2-HF: Nuclear repulsion	825985.400801
FMO2-HF: Total energy	-47808.991977
FMO2-MP2: Total energy	-47949.163819

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:598:SER)

Summations of interaction energy for fragment #1(A:598:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-4.204	-0.369	0.432	-1.573	-2.694	0.002

Interaction energy analysis for fragmet #1(A:598:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.008

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	600	GLU	-1	-0.900	-0.949	2.860	-3.282	-0.904	0.072	-1.060	-1.390	0.002
4	A	601	VAL	0	0.013	0.000	2.754	-0.575	0.621	0.361	-0.434	-1.123	0.000
5	A	602	ALA	0	-0.008	-0.005	4.111	0.337	0.598	-0.001	-0.079	-0.181	0.000
6	A	603	GLU	-1	-0.884	-0.937	6.092	0.371	0.371	0.000	0.000	0.000	0.000
7	A	604	LEU	0	0.048	0.019	7.216	0.030	0.030	0.000	0.000	0.000	0.000
8	A	605	LYS	1	0.960	0.979	6.744	-0.846	-0.846	0.000	0.000	0.000	0.000
9	A	606	LYS	1	1.010	1.020	10.112	-0.247	-0.247	0.000	0.000	0.000	0.000
10	A	607	GLN	0	-0.050	-0.035	11.464	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	608	VAL	0	0.002	0.007	13.233	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	609	GLU	-1	-0.911	-0.955	13.573	0.256	0.256	0.000	0.000	0.000	0.000
13	A	610	SER	0	-0.041	-0.023	16.135	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	611	ALA	0	-0.046	-0.025	17.884	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	612	GLU	-1	-0.831	-0.906	19.164	0.062	0.062	0.000	0.000	0.000	0.000
16	A	613	LEU	0	0.008	0.012	20.522	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	614	LYS	1	0.961	0.964	22.166	-0.084	-0.084	0.000	0.000	0.000	0.000
18	A	615	ASN	0	0.002	0.008	23.687	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	616	GLN	0	-0.028	-0.031	23.379	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	617	ARG	1	0.817	0.876	26.020	-0.070	-0.070	0.000	0.000	0.000	0.000
21	A	618	LEU	0	-0.029	-0.022	27.235	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	619	LYS	1	0.902	0.961	27.448	-0.054	-0.054	0.000	0.000	0.000	0.000
23	A	620	GLU	-1	-0.785	-0.849	31.008	0.051	0.051	0.000	0.000	0.000	0.000
24	A	621	VAL	0	0.008	-0.001	32.193	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	622	PHE	0	-0.002	-0.012	31.274	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	623	GLN	0	-0.002	0.013	35.782	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	624	THR	0	0.010	-0.009	37.419	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	625	LYS	1	0.833	0.906	38.448	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	626	ILE	0	0.013	0.010	38.608	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	627	GLN	0	0.002	-0.005	41.861	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	628	GLU	-1	-0.842	-0.895	42.645	0.030	0.030	0.000	0.000	0.000	0.000
32	A	629	PHE	0	0.024	0.013	44.016	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	630	ARG	1	0.898	0.945	45.856	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	631	LYS	1	0.974	0.990	47.865	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	632	ALA	0	0.004	0.004	48.554	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	633	CYS	0	-0.009	-0.011	49.095	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	634	TYR	0	-0.017	0.014	51.962	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	635	THR	0	-0.056	-0.046	52.828	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	636	LEU	0	-0.049	-0.014	52.209	0.000	0.000	0.000	0.000	0.000	0.000
40	A	637	THR	0	-0.048	-0.039	55.148	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	638	GLY	0	0.065	0.046	57.440	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	639	TYR	0	-0.025	-0.034	57.296	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	640	GLN	0	-0.052	-0.017	52.966	0.001	0.001	0.000	0.000	0.000	0.000
44	A	641	ILE	0	0.009	0.000	51.576	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	642	ASP	-1	-0.833	-0.898	50.598	0.018	0.018	0.000	0.000	0.000	0.000
46	A	643	ILE	0	0.005	0.000	46.339	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	644	THR	0	-0.052	-0.032	49.017	0.000	0.000	0.000	0.000	0.000	0.000
48	A	645	THR	0	0.049	0.012	48.696	0.000	0.000	0.000	0.000	0.000	0.000
49	A	646	GLU	-1	-0.877	-0.937	50.711	0.011	0.011	0.000	0.000	0.000	0.000
50	A	647	ASN	0	0.009	0.004	50.019	0.000	0.000	0.000	0.000	0.000	0.000
51	A	648	GLN	0	0.041	0.022	51.964	0.000	0.000	0.000	0.000	0.000	0.000
52	A	649	TYR	0	0.015	0.011	49.184	0.001	0.001	0.000	0.000	0.000	0.000
53	A	650	ARG	1	0.930	0.961	53.347	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	651	LEU	0	-0.013	-0.007	55.173	0.001	0.001	0.000	0.000	0.000	0.000
55	A	652	THR	0	0.018	0.002	57.204	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	653	SER	0	0.027	0.022	58.606	0.001	0.001	0.000	0.000	0.000	0.000
57	A	654	LEU	0	-0.009	-0.013	58.498	0.000	0.000	0.000	0.000	0.000	0.000
58	A	655	TYR	0	-0.018	-0.014	60.843	0.000	0.000	0.000	0.000	0.000	0.000
59	A	656	ALA	0	-0.004	0.005	63.048	0.000	0.000	0.000	0.000	0.000	0.000
60	A	657	GLU	-1	-0.836	-0.901	64.867	0.010	0.010	0.000	0.000	0.000	0.000
61	A	658	HIS	1	0.828	0.912	66.788	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	659	PRO	0	-0.001	0.011	62.968	0.000	0.000	0.000	0.000	0.000	0.000
63	A	660	GLY	0	0.014	-0.001	61.690	0.000	0.000	0.000	0.000	0.000	0.000
64	A	661	ASP	-1	-0.831	-0.901	62.705	0.011	0.011	0.000	0.000	0.000	0.000
65	A	662	CYS	0	-0.088	-0.054	59.903	0.001	0.001	0.000	0.000	0.000	0.000
66	A	663	LEU	0	0.034	0.036	60.863	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	664	ILE	0	0.023	0.011	57.556	0.001	0.001	0.000	0.000	0.000	0.000
68	A	665	PHE	0	0.033	0.024	57.476	0.000	0.000	0.000	0.000	0.000	0.000
69	A	666	LYS	1	0.840	0.916	55.782	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	667	ALA	0	0.036	0.011	53.196	0.000	0.000	0.000	0.000	0.000	0.000
71	A	668	THR	0	-0.020	-0.018	55.255	0.000	0.000	0.000	0.000	0.000	0.000
72	A	669	SER	0	0.026	0.014	51.914	0.000	0.000	0.000	0.000	0.000	0.000
73	A	670	PRO	0	-0.038	-0.022	47.571	0.000	0.000	0.000	0.000	0.000	0.000
74	A	671	SER	0	-0.019	-0.008	47.347	0.001	0.001	0.000	0.000	0.000	0.000
75	A	672	GLY	0	-0.011	-0.021	49.457	0.000	0.000	0.000	0.000	0.000	0.000
76	A	673	SER	0	-0.050	-0.006	51.662	0.000	0.000	0.000	0.000	0.000	0.000
77	A	674	LYS	1	0.922	0.965	54.022	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	675	MET	0	-0.016	0.001	53.202	0.000	0.000	0.000	0.000	0.000	0.000
79	A	676	GLN	0	-0.028	-0.016	58.466	0.000	0.000	0.000	0.000	0.000	0.000
80	A	677	LEU	0	-0.004	0.006	60.724	0.000	0.000	0.000	0.000	0.000	0.000
81	A	678	LEU	0	-0.040	-0.027	59.298	0.000	0.000	0.000	0.000	0.000	0.000
82	A	679	GLU	-1	-0.863	-0.915	63.303	0.009	0.009	0.000	0.000	0.000	0.000
83	A	680	THR	0	-0.083	-0.061	62.467	0.000	0.000	0.000	0.000	0.000	0.000
84	A	681	GLU	-1	-0.864	-0.942	65.605	0.010	0.010	0.000	0.000	0.000	0.000
85	A	682	PHE	0	0.116	0.049	65.221	0.000	0.000	0.000	0.000	0.000	0.000
86	A	683	SER	0	-0.035	-0.006	66.013	0.000	0.000	0.000	0.000	0.000	0.000
87	A	684	HIS	0	-0.076	-0.061	67.909	0.000	0.000	0.000	0.000	0.000	0.000
88	A	685	THR	0	-0.074	-0.029	70.244	0.000	0.000	0.000	0.000	0.000	0.000
89	A	686	VAL	0	-0.033	-0.020	68.450	0.000	0.000	0.000	0.000	0.000	0.000
90	A	687	GLY	0	0.049	0.018	71.657	0.000	0.000	0.000	0.000	0.000	0.000
91	A	688	GLU	-1	-0.847	-0.927	73.758	0.008	0.008	0.000	0.000	0.000	0.000
92	A	689	LEU	0	0.020	0.006	69.654	0.000	0.000	0.000	0.000	0.000	0.000
93	A	690	ILE	0	0.005	0.005	68.448	0.000	0.000	0.000	0.000	0.000	0.000
94	A	691	GLU	-1	-0.767	-0.855	70.636	0.008	0.008	0.000	0.000	0.000	0.000
95	A	692	VAL	0	-0.021	-0.020	72.908	0.000	0.000	0.000	0.000	0.000	0.000
96	A	693	HIS	0	-0.029	-0.010	68.249	0.000	0.000	0.000	0.000	0.000	0.000
97	A	694	LEU	0	-0.021	-0.010	65.041	0.000	0.000	0.000	0.000	0.000	0.000
98	A	695	ARG	1	0.842	0.917	68.457	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	696	ARG	1	0.805	0.891	71.391	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	697	GLN	0	-0.021	-0.003	69.314	0.000	0.000	0.000	0.000	0.000	0.000
101	A	698	ASP	-1	-0.895	-0.918	65.233	0.011	0.011	0.000	0.000	0.000	0.000
102	A	699	SER	0	0.019	0.004	64.263	0.001	0.001	0.000	0.000	0.000	0.000
103	A	700	ILE	0	0.045	0.012	60.379	0.000	0.000	0.000	0.000	0.000	0.000
104	A	701	PRO	0	-0.002	0.001	59.753	0.000	0.000	0.000	0.000	0.000	0.000
105	A	702	ALA	0	0.031	0.036	62.155	0.000	0.000	0.000	0.000	0.000	0.000
106	A	703	PHE	0	0.039	0.009	64.241	0.000	0.000	0.000	0.000	0.000	0.000
107	A	704	LEU	0	-0.006	-0.008	59.836	0.000	0.000	0.000	0.000	0.000	0.000
108	A	705	SER	0	-0.032	-0.019	63.538	0.000	0.000	0.000	0.000	0.000	0.000
109	A	706	SER	0	0.003	-0.029	64.879	0.000	0.000	0.000	0.000	0.000	0.000
110	A	707	LEU	0	-0.012	0.010	64.740	0.000	0.000	0.000	0.000	0.000	0.000
111	A	708	THR	0	-0.005	-0.003	62.666	0.000	0.000	0.000	0.000	0.000	0.000
112	A	709	LEU	0	-0.022	-0.014	65.764	0.000	0.000	0.000	0.000	0.000	0.000
113	A	710	GLU	-1	-0.811	-0.874	68.897	0.010	0.010	0.000	0.000	0.000	0.000
114	A	711	LEU	0	-0.007	-0.003	65.649	0.000	0.000	0.000	0.000	0.000	0.000
115	A	712	PHE	0	0.000	0.002	66.936	0.000	0.000	0.000	0.000	0.000	0.000
116	A	713	SER	0	-0.059	-0.044	68.887	0.000	0.000	0.000	0.000	0.000	0.000
117	A	714	ARG	1	0.779	0.863	71.500	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	715	GLN	0	-0.060	-0.012	66.384	0.000	0.000	0.000	0.000	0.000	0.000
119	A	716	THR	0	-0.090	-0.038	70.558	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:598:SER)